Cyclooxygenase-1 (COX-1) and Cyclooxygenase (COX-2) are the two major isoforms of cyclooxygenase responsible mainly for production of prostaglandins. The produced prostaglandins exert function in gastric mucosal defense, renal homeostasis, inflammation and pain. In above research work structure based pharmacophoric methodology is employed for designing inhibitors of COX-1 and COX-2. The structure based pharmacophore models were generated. Virtual screening was done to support hit compounds against reference shared feature pharmacophore. Hydrogen bond acceptor, Hydrogen bond donor and aromatic rings/hydrophobicity are the major pharmacophoric features displayed by developed pharmacophore model. The designed hit molecules then screened by employing Lipinski rule of five. The hit molecules which pass from virtual screening filters were docked into the active site of COX-1 and COX-2. They fit appropriately in the pocket of proteins which demonstrated the soundness and stability of ligand compounds. These hit molecules fulfil most of the structural requirements necessary for inhibiting cyclooxygenase. It is suggested that these hit molecules can be used for the treatment of pain and inflammation.